Analysis of Differentially Abundant species

This is an analysis of differentially abundant species in obese rats upon treatment long-term (42 Days) treatment with Sibutramine. To achieve this, DESeq2 was used with the model: ~ number + day

## Number significant =  192

Plot Boxplots for all differentially abundant species

##  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20

##  [1] 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

##  [1] 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

##  [1] 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80

##  [1]  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99
## [20] 100

##  [1] 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
## [20] 120

##  [1] 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
## [20] 140

##  [1] 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
## [20] 160

##  [1] 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
## [20] 180

# Focus on Bacteroides species Below a focus on all the differentially abundant Bacteroides species

Ratio Bacteroidetes/Firmicutes

Below are the details of the R session that was used when this script was executed.

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] DESeq2_1.24.0               SummarizedExperiment_1.14.1
##  [3] DelayedArray_0.10.0         BiocParallel_1.18.1        
##  [5] matrixStats_0.56.0          Biobase_2.44.0             
##  [7] GenomicRanges_1.36.1        GenomeInfoDb_1.20.0        
##  [9] IRanges_2.18.3              S4Vectors_0.22.1           
## [11] BiocGenerics_0.30.0         reshape2_1.4.4             
## [13] ggrepel_0.8.2               vegan_2.5-6                
## [15] lattice_0.20-41             permute_0.9-5              
## [17] phyloseq_1.28.0             ggpubr_0.4.0               
## [19] forcats_0.5.0               stringr_1.4.0              
## [21] dplyr_1.0.2                 purrr_0.3.4                
## [23] readr_1.3.1                 tidyr_1.1.2                
## [25] tibble_3.0.3                ggplot2_3.3.2              
## [27] tidyverse_1.3.0            
## 
## loaded via a namespace (and not attached):
##   [1] readxl_1.3.1           backports_1.1.9        Hmisc_4.4-1           
##   [4] plyr_1.8.6             igraph_1.2.5           splines_3.6.1         
##   [7] digest_0.6.25          foreach_1.5.0          htmltools_0.5.0       
##  [10] fansi_0.4.1            magrittr_1.5           checkmate_2.0.0       
##  [13] memoise_1.1.0          cluster_2.1.0          openxlsx_4.1.5        
##  [16] Biostrings_2.52.0      annotate_1.62.0        modelr_0.1.8          
##  [19] jpeg_0.1-8.1           colorspace_1.4-1       blob_1.2.1            
##  [22] rvest_0.3.6            haven_2.3.1            xfun_0.16             
##  [25] crayon_1.3.4           RCurl_1.98-1.2         jsonlite_1.7.0        
##  [28] genefilter_1.66.0      survival_3.2-3         iterators_1.0.12      
##  [31] ape_5.4-1              glue_1.4.2             gtable_0.3.0          
##  [34] zlibbioc_1.30.0        XVector_0.24.0         car_3.0-9             
##  [37] Rhdf5lib_1.6.3         abind_1.4-5            scales_1.1.1          
##  [40] DBI_1.1.0              rstatix_0.6.0          Rcpp_1.0.5            
##  [43] xtable_1.8-4           htmlTable_2.0.1        foreign_0.8-76        
##  [46] bit_4.0.4              Formula_1.2-3          htmlwidgets_1.5.1     
##  [49] httr_1.4.2             RColorBrewer_1.1-2     ellipsis_0.3.1        
##  [52] farver_2.0.3           pkgconfig_2.0.3        XML_3.99-0.3          
##  [55] nnet_7.3-14            dbplyr_1.4.4           locfit_1.5-9.4        
##  [58] labeling_0.3           tidyselect_1.1.0       rlang_0.4.7           
##  [61] AnnotationDbi_1.46.1   munsell_0.5.0          cellranger_1.1.0      
##  [64] tools_3.6.1            cli_2.0.2              generics_0.0.2        
##  [67] RSQLite_2.2.0          ade4_1.7-15            broom_0.7.0           
##  [70] evaluate_0.14          biomformat_1.12.0      yaml_2.2.1            
##  [73] knitr_1.29             bit64_4.0.5            fs_1.5.0              
##  [76] zip_2.1.1              nlme_3.1-149           xml2_1.3.2            
##  [79] compiler_3.6.1         rstudioapi_0.11        curl_4.3              
##  [82] png_0.1-7              ggsignif_0.6.0         reprex_0.3.0          
##  [85] geneplotter_1.62.0     stringi_1.4.6          Matrix_1.2-18         
##  [88] multtest_2.40.0        vctrs_0.3.4            pillar_1.4.6          
##  [91] lifecycle_0.2.0        cowplot_1.0.0          data.table_1.12.8     
##  [94] bitops_1.0-6           R6_2.4.1               latticeExtra_0.6-29   
##  [97] gridExtra_2.3          rio_0.5.16             codetools_0.2-16      
## [100] MASS_7.3-52            assertthat_0.2.1       rhdf5_2.28.1          
## [103] withr_2.2.0            GenomeInfoDbData_1.2.1 mgcv_1.8-33           
## [106] hms_0.5.3              grid_3.6.1             rpart_4.1-15          
## [109] rmarkdown_2.3          carData_3.0-4          lubridate_1.7.9       
## [112] base64enc_0.1-3